R: Write MArrayLM Object to a File

write.fit {limma}

R Documentation

Write MArrayLM Object to a File

Description

Write a microarray linear model fit to a file.

Usage

write.fit(fit, results = NULL, file, digits = NULL,
          adjust = "none", method = "separate", F.adjust = "none",
          quote = FALSE, sep = "\t", row.names = TRUE, ...)

Arguments

`fit`	object of class `MArrayLM` containing the results of a linear model fit
`results`	object of class `TestResults`
`file`	character string giving name of file
`digits`	integer indicating rounding precision for output values. If `NULL`, then no rounding is done.
`adjust`	character string specifying multiple-testing adjustment method for the t-statistic P-values, e.g., `"BH"`. See `p.adjust` for the available options. If `NULL` or `"none"` then the P-values are not adjusted.
`method`	character string, should the P-value adjustment be `"global"` or `"separate"` for each contrast.
`F.adjust`	character string specifying adjustment method for the F-statistic P-values.
`quote`	logical. If `TRUE`, any character or factor columns will be surrounded by double quotes.
`sep`	the field separator string. Values in the output file will be separated by this string.
`row.names`	logical, whether to include row names in output file.
`...`	other arguments are passed to `write.table`

Details

This function writes a tab-delimited text file containing for each gene (1) the average log2-intensity, (2) the coefficients or contrasts (log2-fold-changes), (3) moderated t-statistics, (4) t-statistic P-values, (5) F-statistic if available, (6) F-statistic P-values if available, (7) classification if available and (8) gene names and annotation.

Value

No value is produced but a file is written to the current working directory.

Author(s)

Gordon Smyth